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Retrieval from the Database of Pre-calcuated Genotyping/Subtyping Results

Virus: HIV-1 / Sequence Type: Nucleotide

Sequence Description: (Link to NCBI GenBank)

Multiple Substitution Correction Algorithm: Jukes-Cantor

All sites that include gaps were deleted.


Gene by Gene Subtype Prediction Summary

Gene Start Stop Length LANL Subtype Major Subtype Nested Analysis Final Decision
env 0 105 58 B B B (Major agrees Nested with high confidence)


Detailed result for env (major) Outlierness: 0.429069 (all), 0.378351 (group)
Subtype Posterior Probability
01_AE 0.00000112736
A 0.00000227953
B 0.729853
C 0.240296
D 0.00000000153316
F 0.0148372
G 0.0149394
H 0.00000556226
J 0.0000000159997
K 0.0000662082

Cross-Validation of Discriminant Models
Miss-Classification Rate: 215 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   G   H   J
    01_AE    65   1   3   0   0   0   0   1
    A         0  76   1   2   0   1   1   1
    B         1   0 412  39   1   1   0   0
    C         0   5 107 351   1   0   0   0
    D         0   0   6   3  51   0   0   0
    F         0   0   8   8   0   0   0   0
    G         0   2  10   6   0   5   0   0
    H         0   3   0   0   0   0   0   0
    J         0   0   0   0   0   0   0   0
    K         0   0   1   1   0   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (nested) Outlierness: 0.489189 (all), 0.478335 (group)
Subtype Posterior Probability
02_AG 0.000000224419
03_AB 0.0000599243
04_cpx 0.0000000106934
05_DF 0.000168061
06_cpx 0.00126073
07_BC 0.000790926
08_BC 0.000149913
09_cpx 0.00000017949
10_CD 0.0000116859
11_cpx 0.0000000184446
12_BF 0.00171839
13_cpx 0.000000126905
14_BG 0.0146593
15_01B 0.000386008
B 0.718164
C 0.22548
F 0.00945134
G 0.0276995

Cross-Validation of Discriminant Models
Miss-Classification Rate: 262 / 1075 at 10 Dimensional MDS
         Predicted
Objective 02_AG 03_AB 04_cpx 08_BC 09_cpx 10_CD 11_cpx 13_cpx   B   C   G
   02_AG     45     0      1     0      0     0      7      0   0   0   2
   03_AB      0     0      0     0      0     0      0      0   0   0   0
   04_cpx     3     0      0     0      0     0      0      0   0   0   0
   05_DF      0     0      0     0      0     0      0      0   0   3   0
   06_cpx     0     0      0     0      0     0      0      0   0   0   6
   07_BC      0     0      0     0      0     0      0      0   1   9   0
   08_BC      0     0      0     0      0     0      0      0   0   2   0
   09_cpx     3     0      0     0      0     1      0      0   0   0   0
   10_CD      0     0      0     0      0     0      0      0   2   1   0
   11_cpx     4     0      0     0      0     0      6      1   0   0   0
   12_BF      0     0      0     0      0     0      0      0   2   8   0
   13_cpx     1     0      0     0      0     0      1      0   0   0   1
   14_BG      0     0      0     0      0     0      0      0   2   1   0
   15_01B     0     0      0     0      0     0      0      0   4   0   0
   B          0     1      0     0      0     3      1      0 407  42   0
   C          1     0      0     1      3     3      1      0 104 350   1
   F          0     0      0     0      0     0      0      0   8   8   0
   G          2     0      0     0      0     0      0      0   6  10   5

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Copyrighted by Bio-Data Mining Lab, Department of Bioinformatics and Life Sciences, Soongsil University, Seoul, Korea